Correlation between gene mutation status and molecular subtypes
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 12 genes and 10 molecular subtypes across 283 patients, 20 significant findings detected with P value < 0.05 and Q value < 0.25.

  • EGFR mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF', and 'RPPA_CHIERARCHICAL'.

  • IDH1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MIR_CNMF',  'MIR_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • NF1 mutation correlated to 'METHLYATION_CNMF'.

  • WNT2 mutation correlated to 'MRNA_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 12 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 20 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
IDH1 14 (5%) 269 9.83e-05
(0.0105) 		1.01e-06
(0.000116) 		2.52e-05
(0.00277) 		2.61e-06
(0.000295) 		1.24e-05
(0.00137) 		0.00181
(0.179) 		0.00352
(0.335) 		0.0203
(1.00) 		0.000712
(0.0741) 		0.00263
(0.253)
TP53 79 (28%) 204 0.000696
(0.073) 		0.000488
(0.0518) 		0.0015
(0.151) 		0.00216
(0.212) 		3.07e-06
(0.000344) 		6.87e-05
(0.00748) 		0.0392
(1.00) 		0.00919
(0.836) 		0.00179
(0.179) 		0.0362
(1.00)
EGFR 74 (26%) 209 0.00719
(0.669) 		0.0317
(1.00) 		0.511
(1.00) 		0.233
(1.00) 		1.07e-07
(1.24e-05) 		0.00118
(0.122) 		7.77e-05
(0.00839) 		1.69e-06
(0.000193) 		0.0425
(1.00) 		0.347
(1.00)
NF1 29 (10%) 254 0.086
(1.00) 		0.0574
(1.00) 		0.027
(1.00) 		0.847
(1.00) 		0.00781
(0.719) 		0.00136
(0.139) 		0.227
(1.00) 		0.125
(1.00) 		0.566
(1.00) 		0.915
(1.00)
WNT2 5 (2%) 278 0.151
(1.00) 		0.00235
(0.228) 		0.431
(1.00) 		0.134
(1.00) 		1
(1.00) 		0.0416
(1.00) 		0.423
(1.00)
PIK3R1 32 (11%) 251 0.74
(1.00) 		0.708
(1.00) 		0.2
(1.00) 		0.134
(1.00) 		0.0207
(1.00) 		0.436
(1.00) 		0.974
(1.00) 		0.253
(1.00) 		0.406
(1.00) 		0.602
(1.00)
BRAF 6 (2%) 277 0.768
(1.00) 		0.352
(1.00) 		0.318
(1.00) 		0.0224
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.0781
(1.00) 		0.791
(1.00) 		1
(1.00)
PTEN 87 (31%) 196 0.116
(1.00) 		0.431
(1.00) 		0.0273
(1.00) 		0.26
(1.00) 		0.588
(1.00) 		0.88
(1.00) 		0.371
(1.00) 		0.384
(1.00) 		0.274
(1.00) 		0.195
(1.00)
PIK3CA 30 (11%) 253 0.711
(1.00) 		0.62
(1.00) 		0.489
(1.00) 		0.948
(1.00) 		0.549
(1.00) 		0.164
(1.00) 		0.754
(1.00) 		0.286
(1.00) 		0.262
(1.00) 		0.838
(1.00)
RB1 24 (8%) 259 0.0365
(1.00) 		0.0117
(1.00) 		0.135
(1.00) 		0.792
(1.00) 		0.0222
(1.00) 		0.167
(1.00) 		0.493
(1.00) 		0.691
(1.00) 		0.0818
(1.00) 		0.0754
(1.00)
STAG2 12 (4%) 271 0.392
(1.00) 		0.132
(1.00) 		0.717
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.00694
(0.652) 		0.184
(1.00) 		0.479
(1.00) 		0.771
(1.00)
TPTE2 8 (3%) 275 0.46
(1.00) 		1
(1.00) 		0.468
(1.00) 		0.822
(1.00) 		0.266
(1.00) 		0.241
(1.00) 		0.624
(1.00) 		0.409
(1.00) 		0.376
(1.00) 		0.741
(1.00)
'EGFR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00719 (Fisher's exact test), Q value = 0.67

Table S1.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
EGFR MUTATED 20 7 31 10
EGFR WILD-TYPE 49 36 43 44

Figure S1.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EGFR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
EGFR MUTATED 20 15 33
EGFR WILD-TYPE 34 67 71

Figure S2.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
EGFR MUTATED 22 27 8 17
EGFR WILD-TYPE 55 66 37 43
'EGFR MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
EGFR MUTATED 30 17 27
EGFR WILD-TYPE 67 67 67
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 1.07e-07 (Fisher's exact test), Q value = 1.2e-05

Table S5.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
EGFR MUTATED 14 50 8
EGFR WILD-TYPE 66 64 71

Figure S3.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.12

Table S6.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
EGFR MUTATED 5 15 1
EGFR WILD-TYPE 29 27 31

Figure S4.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 7.77e-05 (Fisher's exact test), Q value = 0.0084

Table S7.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
EGFR MUTATED 13 5 16 2
EGFR WILD-TYPE 28 33 15 31

Figure S5.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1.69e-06 (Fisher's exact test), Q value = 0.00019

Table S8.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
EGFR MUTATED 24 6 6
EGFR WILD-TYPE 23 22 62

Figure S6.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
EGFR MUTATED 8 22 15
EGFR WILD-TYPE 36 40 20

Figure S7.  Get High-res Image Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
EGFR MUTATED 22 8 15
EGFR WILD-TYPE 39 13 44
'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PIK3R1 MUTATED 7 2 8 5
PIK3R1 WILD-TYPE 62 41 66 49
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
PIK3R1 MUTATED 6 6 10
PIK3R1 WILD-TYPE 48 76 94
'PIK3R1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PIK3R1 MUTATED 12 13 4 3
PIK3R1 WILD-TYPE 65 80 41 57
'PIK3R1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
PIK3R1 MUTATED 14 12 6
PIK3R1 WILD-TYPE 83 72 88
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
PIK3R1 MUTATED 3 15 13
PIK3R1 WILD-TYPE 77 99 66

Figure S8.  Get High-res Image Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
PIK3R1 MUTATED 7 8 3
PIK3R1 WILD-TYPE 27 34 29
'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.974 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PIK3R1 MUTATED 7 6 4 5
PIK3R1 WILD-TYPE 34 32 27 28
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
PIK3R1 MUTATED 4 5 13
PIK3R1 WILD-TYPE 43 23 55
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PIK3R1 MUTATED 5 6 1
PIK3R1 WILD-TYPE 39 56 34
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
PIK3R1 MUTATED 7 1 4
PIK3R1 WILD-TYPE 54 20 55
'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
BRAF MUTATED 1 1 2 0
BRAF WILD-TYPE 68 42 72 54
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
BRAF MUTATED 1 0 3
BRAF WILD-TYPE 53 82 101
'BRAF MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
BRAF MUTATED 2 1 0 3
BRAF WILD-TYPE 75 92 45 57
'BRAF MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
BRAF MUTATED 0 1 5
BRAF WILD-TYPE 97 83 89

Figure S9.  Get High-res Image Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
BRAF MUTATED 1 2 3
BRAF WILD-TYPE 79 112 76
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
BRAF MUTATED 1 1 0 1
BRAF WILD-TYPE 40 37 31 32
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0781 (Fisher's exact test), Q value = 1

Table S27.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 46 26 68
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 43 60 35
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
BRAF MUTATED 2 0 1
BRAF WILD-TYPE 59 21 58
'IDH1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 9.83e-05 (Fisher's exact test), Q value = 0.011

Table S30.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
IDH1 MUTATED 1 3 0 9
IDH1 WILD-TYPE 68 40 74 45

Figure S10.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1.01e-06 (Fisher's exact test), Q value = 0.00012

Table S31.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
IDH1 MUTATED 0 13 0
IDH1 WILD-TYPE 54 69 104

Figure S11.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.0028

Table S32.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
IDH1 MUTATED 0 13 1 0
IDH1 WILD-TYPE 77 80 44 60

Figure S12.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'IDH1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 2.61e-06 (Fisher's exact test), Q value = 3e-04

Table S33.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
IDH1 MUTATED 1 13 0
IDH1 WILD-TYPE 96 71 94

Figure S13.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0014

Table S34.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
IDH1 MUTATED 2 0 11
IDH1 WILD-TYPE 78 114 68

Figure S14.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00181 (Fisher's exact test), Q value = 0.18

Table S35.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
IDH1 MUTATED 0 0 5
IDH1 WILD-TYPE 34 42 27

Figure S15.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.33

Table S36.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
IDH1 MUTATED 1 6 0 0
IDH1 WILD-TYPE 40 32 31 33

Figure S16.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
IDH1 MUTATED 0 0 7
IDH1 WILD-TYPE 47 28 61

Figure S17.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000712 (Fisher's exact test), Q value = 0.074

Table S38.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
IDH1 MUTATED 7 0 1
IDH1 WILD-TYPE 37 62 34

Figure S18.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.25

Table S39.  Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
IDH1 MUTATED 0 0 8
IDH1 WILD-TYPE 61 21 51

Figure S19.  Get High-res Image Gene #4: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.000696 (Fisher's exact test), Q value = 0.073

Table S40.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TP53 MUTATED 16 19 11 22
TP53 WILD-TYPE 53 24 63 32

Figure S20.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000488 (Fisher's exact test), Q value = 0.052

Table S41.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
TP53 MUTATED 7 35 26
TP53 WILD-TYPE 47 47 78

Figure S21.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.15

Table S42.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TP53 MUTATED 12 39 10 18
TP53 WILD-TYPE 65 54 35 42

Figure S22.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.00216 (Fisher's exact test), Q value = 0.21

Table S43.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
TP53 MUTATED 19 36 24
TP53 WILD-TYPE 78 48 70

Figure S23.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 3.07e-06 (Fisher's exact test), Q value = 0.00034

Table S44.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
TP53 MUTATED 35 15 28
TP53 WILD-TYPE 45 99 51

Figure S24.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 6.87e-05 (Fisher's exact test), Q value = 0.0075

Table S45.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
TP53 MUTATED 4 5 17
TP53 WILD-TYPE 30 37 15

Figure S25.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TP53 MUTATED 12 17 4 10
TP53 WILD-TYPE 29 21 27 23

Figure S26.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.84

Table S47.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
TP53 MUTATED 7 8 28
TP53 WILD-TYPE 40 20 40

Figure S27.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.18

Table S48.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TP53 MUTATED 23 13 8
TP53 WILD-TYPE 21 49 27

Figure S28.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0362 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
TP53 MUTATED 19 2 23
TP53 WILD-TYPE 42 19 36

Figure S29.  Get High-res Image Gene #5: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 1

Table S50.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PTEN MUTATED 25 10 18 22
PTEN WILD-TYPE 44 33 56 32
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
PTEN MUTATED 13 28 34
PTEN WILD-TYPE 41 54 70
'PTEN MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PTEN MUTATED 30 19 18 20
PTEN WILD-TYPE 47 74 27 40

Figure S30.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'PTEN MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
PTEN MUTATED 26 32 29
PTEN WILD-TYPE 71 52 65
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
PTEN MUTATED 28 32 25
PTEN WILD-TYPE 52 82 54
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
PTEN MUTATED 10 14 9
PTEN WILD-TYPE 24 28 23
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PTEN MUTATED 12 14 6 12
PTEN WILD-TYPE 29 24 25 21
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S57.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
PTEN MUTATED 11 9 24
PTEN WILD-TYPE 36 19 44
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PTEN MUTATED 10 23 12
PTEN WILD-TYPE 34 39 23
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
PTEN MUTATED 24 4 17
PTEN WILD-TYPE 37 17 42
'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S60.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
PIK3CA MUTATED 6 6 10 5
PIK3CA WILD-TYPE 63 37 64 49
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
PIK3CA MUTATED 7 7 13
PIK3CA WILD-TYPE 47 75 91
'PIK3CA MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
PIK3CA MUTATED 10 11 2 6
PIK3CA WILD-TYPE 67 82 43 54
'PIK3CA MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
PIK3CA MUTATED 11 8 10
PIK3CA WILD-TYPE 86 76 84
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S64.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
PIK3CA MUTATED 6 12 10
PIK3CA WILD-TYPE 74 102 69
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
PIK3CA MUTATED 2 5 7
PIK3CA WILD-TYPE 32 37 25
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S66.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
PIK3CA MUTATED 3 5 2 4
PIK3CA WILD-TYPE 38 33 29 29
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S67.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
PIK3CA MUTATED 2 3 9
PIK3CA WILD-TYPE 45 25 59
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
PIK3CA MUTATED 6 3 2
PIK3CA WILD-TYPE 38 59 33
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
PIK3CA MUTATED 4 2 5
PIK3CA WILD-TYPE 57 19 54
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 1

Table S70.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
RB1 MUTATED 11 2 3 2
RB1 WILD-TYPE 58 41 71 52

Figure S31.  Get High-res Image Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
RB1 MUTATED 1 3 14
RB1 WILD-TYPE 53 79 90

Figure S32.  Get High-res Image Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
RB1 MUTATED 11 4 3 6
RB1 WILD-TYPE 66 89 42 54
'RB1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
RB1 MUTATED 7 8 9
RB1 WILD-TYPE 90 76 85
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
RB1 MUTATED 10 4 10
RB1 WILD-TYPE 70 110 69

Figure S33.  Get High-res Image Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
RB1 MUTATED 5 1 2
RB1 WILD-TYPE 29 41 30
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
RB1 MUTATED 3 1 2 4
RB1 WILD-TYPE 38 37 29 29
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
RB1 MUTATED 2 2 6
RB1 WILD-TYPE 45 26 62
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0818 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
RB1 MUTATED 1 8 1
RB1 WILD-TYPE 43 54 34
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0754 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
RB1 MUTATED 8 0 2
RB1 WILD-TYPE 53 21 57
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.086 (Fisher's exact test), Q value = 1

Table S80.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
NF1 MUTATED 11 4 4 2
NF1 WILD-TYPE 58 39 70 52
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
NF1 MUTATED 4 3 14
NF1 WILD-TYPE 50 79 90
'NF1 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
NF1 MUTATED 12 3 5 8
NF1 WILD-TYPE 65 90 40 52

Figure S34.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

'NF1 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
NF1 MUTATED 9 10 9
NF1 WILD-TYPE 88 74 85
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.72

Table S84.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
NF1 MUTATED 5 8 16
NF1 WILD-TYPE 75 106 63

Figure S35.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.14

Table S85.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
NF1 MUTATED 10 2 1
NF1 WILD-TYPE 24 40 31

Figure S36.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
NF1 MUTATED 7 3 1 5
NF1 WILD-TYPE 34 35 30 28
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
NF1 MUTATED 2 5 9
NF1 WILD-TYPE 45 23 59
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
NF1 MUTATED 2 5 4
NF1 WILD-TYPE 42 57 31
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
NF1 MUTATED 5 2 4
NF1 WILD-TYPE 56 19 55
'STAG2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 1

Table S90.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
STAG2 MUTATED 4 3 1 2
STAG2 WILD-TYPE 65 40 73 52
'STAG2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
STAG2 MUTATED 5 2 3
STAG2 WILD-TYPE 49 80 101
'STAG2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
STAG2 MUTATED 4 5 2 1
STAG2 WILD-TYPE 73 88 43 59
'STAG2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
STAG2 MUTATED 7 3 2
STAG2 WILD-TYPE 90 81 92
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
STAG2 MUTATED 4 5 3
STAG2 WILD-TYPE 76 109 76
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
STAG2 MUTATED 1 3 1
STAG2 WILD-TYPE 33 39 31
'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.65

Table S96.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
STAG2 MUTATED 0 2 0 5
STAG2 WILD-TYPE 41 36 31 28

Figure S37.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
STAG2 MUTATED 1 0 6
STAG2 WILD-TYPE 46 28 62
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S98.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
STAG2 MUTATED 1 3 3
STAG2 WILD-TYPE 43 59 32
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
STAG2 MUTATED 2 1 4
STAG2 WILD-TYPE 59 20 55
'WNT2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S100.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
WNT2 MUTATED 0 1 3 0
WNT2 WILD-TYPE 69 42 71 54
'WNT2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.23

Table S101.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
WNT2 MUTATED 4 0 0
WNT2 WILD-TYPE 50 82 104

Figure S38.  Get High-res Image Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'WNT2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
WNT2 MUTATED 0 2 1 2
WNT2 WILD-TYPE 77 91 44 58
'WNT2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 1

Table S103.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
WNT2 MUTATED 4 0 1
WNT2 WILD-TYPE 93 84 93
'WNT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S104.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
WNT2 MUTATED 2 2 1
WNT2 WILD-TYPE 78 112 78
'WNT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 1

Table S105.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
WNT2 MUTATED 0 0 2 3
WNT2 WILD-TYPE 41 38 29 30

Figure S39.  Get High-res Image Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

'WNT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S106.  Gene #11: 'WNT2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
WNT2 MUTATED 3 0 2
WNT2 WILD-TYPE 44 28 66
'TPTE2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S107.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 69 43 74 54
TPTE2 MUTATED 1 3 2 2
TPTE2 WILD-TYPE 68 40 72 52
'TPTE2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S108.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 82 104
TPTE2 MUTATED 2 3 3
TPTE2 WILD-TYPE 52 79 101
'TPTE2 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S109.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 77 93 45 60
TPTE2 MUTATED 3 1 1 3
TPTE2 WILD-TYPE 74 92 44 57
'TPTE2 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 97 84 94
TPTE2 MUTATED 2 3 3
TPTE2 WILD-TYPE 95 81 91
'TPTE2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 114 79
TPTE2 MUTATED 4 1 2
TPTE2 WILD-TYPE 76 113 77
'TPTE2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 42 32
TPTE2 MUTATED 2 0 2
TPTE2 WILD-TYPE 32 42 30
'TPTE2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 41 38 31 33
TPTE2 MUTATED 1 1 0 2
TPTE2 WILD-TYPE 40 37 31 31
'TPTE2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 28 68
TPTE2 MUTATED 0 1 3
TPTE2 WILD-TYPE 47 27 65
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S115.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 44 62 35
TPTE2 MUTATED 3 3 0
TPTE2 WILD-TYPE 41 59 35
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 21 59
TPTE2 MUTATED 3 0 3
TPTE2 WILD-TYPE 58 21 56
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = GBM-TP.transferedmergedcluster.txt

  • Number of patients = 283

  • Number of significantly mutated genes = 12

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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